[galaxy-dev] casOT wrapper
Hi, I was just wondering if anyone has put any work in to developing wrappers for casOT: http://eendb.zfgenetics.org/casot/index.php Couldn't see anything in the toolshed. If not I'll have a go myself. Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] toolshed image file location problem
Ok thanks, I will vote it up, and for now try to manually edit lib/tool_shed/util/shed_util_common.py Thanks On 20 January 2014 15:51, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Eric, please see the following ticket for it and vote it up :) https://trello.com/c/dWvkfBKC Sorry that there is no fix for it yet, Bjoern e the actual image is located at ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] numpy and scipy
Are numpy and scipy included with the standard python modules/eggs supplied by galaxy? David Hoover Helix Systems Staff ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] numpy and scipy
Hi David, numpy and scipy are not included as modules with the galaxy distribution, but you can use the repositories from the toolshed and depend on them. http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 An example usage is here: https://github.com/bgruening/galaxytools/blob/master/statistics/tool_dependencies.xml Hope that helps! Bjoern Are numpy and scipy included with the standard python modules/eggs supplied by galaxy? David Hoover Helix Systems Staff ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] ToolShed slow? esp uploading
Hi guys, I'm currently trying to update the blast_datatypes on the main tool shed (thanks Nicola for the reminder), http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes Having clicked upload it is stuck at: [Warning] Upload a single file or tarball. Uploading may take a while, depending upon the size of the file. Wait until a message is displayed in your browser after clicking the Upload button below. At what point do I give up and retry? Its been 8 minutes since I thought to start timing, call it 10 minutes so far... In other tabs, the Tool Shed is running but the response feels more sluggish than usual (just browsing tools etc). Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ToolShed slow? esp uploading
On Tue, Jan 21, 2014 at 6:19 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi guys, I'm currently trying to update the blast_datatypes on the main tool shed (thanks Nicola for the reminder), http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes Having clicked upload it is stuck at: [Warning] Upload a single file or tarball. Uploading may take a while, depending upon the size of the file. Wait until a message is displayed in your browser after clicking the Upload button below. At what point do I give up and retry? Its been 8 minutes since I thought to start timing, call it 10 minutes so far... I gave up after ~20 minutes, closed that tab, and tried again. It worked perfectly twice in a row (blast_datatypes v0.0.17 and v0.0.18). Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Can't view file_name in histories via API unless admin?
Hey Neil, While poking through a few options for you, I remembered we added 'expose_dataset_path' to universe_wsgi.ini. If you're comfortable with users knowing full pathnames, you can enable this 'expose_dataset_path = True' and everyone will be able to see their full paths. -Dannon On Sat, Jan 18, 2014 at 9:37 PM, neil.burd...@csiro.au wrote: Thanks Dannon, Apologies for the length of the email, I'll try and be as succint as possible. I am using Galaxy as a tool for medical image processing. We have a number of organisations (researchers and clinicians ) who would like to use the medical imaging tools we have developed, so are using Galaxy to make them available to the whole community. The researchers and clinicians would just prefer to select a file press execute and then everything would be done i.e. uploaded, processed, results returned. I've managed to achieve this (using a test account which is an admin user). In summary, using John Chilton's multi-file branch of Galaxy, the user can select multiple files and then presses execute. The code(and workflows) then upload all the files selected, splits them into smaller datasets (as the tool only needs 2 input files - for example the user may upload 0179_AV45.hdr, 0179_AV45.img, 0279_AV45.hdr, 0179_AV45.img, 0199_AV45.hdr and 0199_AV45.img, given these 6 input files; 3 datasets will be created based on the filenames i.e. 0199_AV45.hdr and 0199_AV45.img will be in one dataset etc). Another tool is responsible for batching and executing the medical imaging tool with each of these 3 datasets, and finally all the results are returned and then emailed back to the user ( so no user interaction is required other than selecting files and pressing execute) This all worked fine as an admin user, but as a non admin user we are unable to get the file_name from the /api/histories/contents/ etc... being upload for the dataset_id.dat. We need to get the history id of that datase_id.dat filename so we can execute the workflow. As admin, I have a script that is able to get get all the files uploaded (under/histories/contents/etc ...) and then examine each history id to get the file_name and match it with the name that we just uploaded. From this we could then get the history_id. But seen as we can't get hold of the file_name unless your an admin user. Do you know how we can get hold of the history_id of the filename i.e. we can't just assume it's the last entry in /history/contents. So given only a database_'id'.dat filename how can I get the history id dynamically with no user interaction and not being an admin user? Thanks for any help Neil p.s. do you know where in the code it stops file_name from being displayed (using the scripts/api/display.py script) -- *From:* Dannon Baker [dannon.ba...@gmail.com] *Sent:* Saturday, January 18, 2014 12:34 AM *To:* Burdett, Neil (CCI, Herston - RBWH) *Cc:* charles.girar...@embl.de; Galaxy Dev *Subject:* Re: [galaxy-dev] Can't view file_name in histories via API unless admin? Hi Niel, Galaxy does not expose filepaths to non-admin users intentionally. For executing a workflow with that particular script, the 'file_id' in question in that example should be an hda, which is what api/history/contents will display for your users as the 'id' for each history item. -Dannon On Fri, Jan 17, 2014 at 6:12 AM, neil.burd...@csiro.au wrote: Hi Charles, not a problem. In my previous post I specified the command line: /home/galaxy/milxcloud/scripts/api/display.py api_key http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 The api_key in your question refers to the api_key of an admin user, however, the history_id (ebfb8f50c6abde6d) refers to a history not owned by the admin user using the unique api_key i.e. another user, hence the error message I hope that answers your question? Neil From: Charles Girardot [charles.girar...@embl.de] Sent: Friday, January 17, 2014 6:31 PM To: Burdett, Neil (CCI, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Can't view file_name in histories via API unless admin? Hi Neil, sorry, this is not an answer to your post, I hope you won t mind me stepping in your thread this way. Your message kept my attention because of your note: I am surprised by the error message you report when trying to use an admin API key. How does galaxy know the user who is making the call? Sorry if I am missing the obvious bw Charles On 17 Jan 2014, at 07:35, neil.burd...@csiro.au wrote: Hi, it seems that the entry file_name: does not appear when running the command /home/galaxy/milxcloud/scripts/api/display.py api_key http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 unless you are stated as as admin
[galaxy-dev] Error when searching for tools in local instance.
Dear All, When I go to my Galaxy Distibution I go the following place: Admin - Manage installed tool shed repositories When I search for a tool in here with the provided search bar, I get the following (I believe this is a bug): URL: https://galaxy.tamu.edu/admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_checkboxes=falsef-deleted=Falsef-free-text-search=search File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 229 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 153 in browse_repositories return self.installed_repository_grid( trans, **kwd ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 138 in __call__ query = column.filter( trans, trans.user, query, column_filter ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 616 in filter clause_list.append( column.get_filter( trans, user, column_filter ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 400 in get_filter return self.get_single_filter( user, column_filter ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 413 in get_single_filter if self.key.find( '.' ) -1: AttributeError: 'NoneType' object has no attribute 'find' How would I go to fix this. Thank you, --Ricardo Perez ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] setting up the drmaa for sge
Hi all, I have been trying to set up my galaxy instance to use SGE -- I created a job_conf.xml using the sample as a model and updated the galaxy user bashrc with the DRMAA_LIBRARY_PATH export DRMAA_LIBRARY_PATH=/home/sge/lib/lx26-amd64/libdrmaa.so But when I try to add data to a library I get the error: Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. Not too comforting since I am the administrator. The error in the log says: galaxy.jobs.handler DEBUG 2014-01-21 14:57:39,478 (2) Dispatching to drmaa runner galaxy.jobs.handler ERROR 2014-01-21 14:57:39,479 put(): (2) Invalid job runner: drmaa What does that mean, Invalid job runner? Does this mean I have an error in my job_conf.xml? Here is my job_conf.xml ?xml version=1.0? job_conf plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin. -- plugin id=sge type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ /plugins handlers default=handlers !-- Additional job handlers - the id should match the name of a [server:id] in universe_wsgi.ini. -- handler id=main tags=handlers/ /handlers destinations default=sge_default !-- Destinations define details about remote resources and how jobs should be executed on those remote resources. -- destination id=sge_default runner=drmaa/ !-- Define parameters that are native to the job runner plugin. -- /destinations /job_conf Thanks for your help! ~~~ Brandi Cantarel, PhD Bioinformatics Research Scientist Baylor Institute for Immunology Research Baylor Health Care System 214-820-9064 (office) ** This e-mail may contain confidential and/or privileged information. This information is intended only for the use of the individual(s) and entity(ies) to whom it is addressed. If you are the intended recipient, further disclosures are prohibited without proper authorization. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden and possibly a violation of federal or state law and regulations. Baylor Health Care System, its subsidiaries, and affiliates hereby claim all applicable privileges related to this information. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error when searching for tools in local instance.
Hi Ricardo, Are you using the newest version from the stable branch or from default? Thanks, Sam On Tue, Jan 21, 2014 at 3:53 PM, Perez, Ricardo ricky_...@neo.tamu.eduwrote: Dear All, When I go to my Galaxy Distibution I go the following place: Admin - Manage installed tool shed repositories When I search for a tool in here with the provided search bar, I get the following (I believe this is a bug): URL: https://galaxy.tamu.edu/admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_checkboxes=falsef-deleted=Falsef-free-text-search=search File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 229 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 153 in browse_repositories return self.installed_repository_grid( trans, **kwd ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 138 in __call__ query = column.filter( trans, trans.user, query, column_filter ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 616 in filter clause_list.append( column.get_filter( trans, user, column_filter ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 400 in get_filter return self.get_single_filter( user, column_filter ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 413 in get_single_filter if self.key.find( '.' ) -1: AttributeError: 'NoneType' object has no attribute 'find' How would I go to fix this. Thank you, --Ricardo Perez ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] dbkey in cuffdiff
Hello, I am using cuffdiff with the bias correction. I have uploaded the S.pombe genome file and changed the database/build option to the S.pombe genome and saved it. Afterwards I used cuffmerge and then I wanted to use cuffdiff. However, it seems that the dbkey for pombe is not recognised, but as it is a drop down menu, there is no way to change it. I get the following error in the logfile: cuffdiff: unrecognized option `--dbkey=Schizosaccharomyces_pombe_1.1' I would greatly appreciate your help! All the best wishes, Rita ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Import workflows via API
Hi Nicola,
I've merged your changes into my version of the galaxy code
(slightly older than galaxy-central) I believe, however, I get the following
error when I try and execute your script:
Traceback (most recent call last):
File get_wfs.py, line 13, in module
common.post(api_key, 'http://barium-rbh:9100/extras/api/workflows/import',
data)
File /home/galaxy/milxcloud/scripts/api/common.py, line 48, in post
return simplejson.loads( urllib2.urlopen( req ).read() )
File /usr/lib/python2.7/urllib2.py, line 126, in urlopen
return _opener.open(url, data, timeout)
File /usr/lib/python2.7/urllib2.py, line 406, in open
response = meth(req, response)
File /usr/lib/python2.7/urllib2.py, line 519, in http_response
'http', request, response, code, msg, hdrs)
File /usr/lib/python2.7/urllib2.py, line 444, in error
return self._call_chain(*args)
File /usr/lib/python2.7/urllib2.py, line 378, in _call_chain
result = func(*args)
File /usr/lib/python2.7/urllib2.py, line 527, in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
urllib2.HTTPError: HTTP Error 500: Internal Server Error
so I printed out the some lines in common.py
def post( api_key, url, data ):
# Do the actual POST.
url = make_url( api_key, url )
print URL is %s % url
URL is
http://barium-rbh:9100/extras/api/workflows/import?key=34ee80757f0d03de36e33a1676d245e4
the script is:
import sys
#sys.path.insert(1, 'milxcloud/scripts/api')
import common
api_key = '34ee80757f0d03de36e33a1676d245e4'
workflows = common.get(api_key,
'http://barium-rbh:9100/api/workflows?show_published=True')
print workflows
published_workflow_ids = [str(workflow[u'id']) for workflow in workflows if
bool(workflow[u'published'])]
print published_workflow_ids
for pw_id in published_workflow_ids:
data = {}
data['workflow_id'] = pw_id
common.post(api_key, 'http://barium-rbh:9100/extras/api/workflows/import',
data)
and I run it from ~/scripts/api
The output from the script is :
python get_wfs.py
[{'name': 'SUVR', 'tags': [], 'url': '/extras/api/workflows/f2db41e1fa331b3e',
'published': True, 'model_class': 'StoredWorkflow', 'id': 'f2db41e1fa331b3e'},
{'name': 'processSUVRData', 'tags': [], 'url':
'/extras/api/workflows/f597429621d6eb2b', 'published': True, 'model_class':
'StoredWorkflow', 'id': 'f597429621d6eb2b'}]
['f2db41e1fa331b3e', 'f597429621d6eb2b']
URL is
http://barium-rbh:9100/extras/api/workflows/import?key=34ee80757f0d03de36e33a1676d245e4
Any ideas why the import maybe failing?
Thanks
Neil
From: Nicola Soranzo [sora...@crs4.it]
Sent: Monday, January 20, 2014 9:03 PM
To: Burdett, Neil (CCI, Herston - RBWH)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: Import workflows via API
Hi Neil,
to import all published workflows you can use a script like this:
import sys
sys.path.insert(1, 'galaxy-central/scripts/api')
import common
api_key = 'YOUR_USER_API_KEY'
workflows = common.get(api_key,
'http://YOUR_SERVER/api/workflows?show_published=True')
published_workflow_ids = [str(workflow[u'id']) for workflow in
workflows if bool(workflow[u'published'])]
for pw_id in published_workflow_ids:
data['workflow_id'] = pw_id
common.post(api_key, 'http://YOUR_SERVER/api/workflows/import',
data)
Nicola
Il 2014-01-19 03:12 neil.burd...@csiro.au ha scritto:
Hi Nicola,
that is exactly what I'm looking for, however, how do
I execute the script/tool? I would like to import all published
workflows. What is the name of the script to run and the arguments ?
Can you give an example please?
Thanks again
Neil
Date: Fri, 17 Jan 2014 11:36:03 +0100
From: Nicola Soranzo sora...@crs4.it
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Import workflows via API
Message-ID: d834d247437269704a26e8bbf8f67...@crs4.it
Content-Type: text/plain; charset=UTF-8; format=flowed
Il 2014-01-17 06:45 neil.burd...@csiro.au ha scritto:
Hi,
I execute workflows via the API. However, if I want another user to
use my workflows, I can publish my workflows, but the new user then
has to go on to the web browser and import this workflow.
Is there a method/script which I can call via the API which can
import
all available (published) workflows so the user doesn't have to
click
a button on the web browser import workflow ?
Thanks for any help
Hi Neil,
you are very lucky, just yesterday my pull request implementing
exactly
this has been merged in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/pull-request/298/api-display-and-import-workflows-shared-by/diff
and is also available in BioBlend thanks to my colleague Simone Leo:
https://github.com/afgane/bioblend/pull/51
Best,
Nicola
--
Nicola Soranzo, Ph.D.
Bioinformatics Program, CRS4
Loc. Piscina Manna, 09010 Pula (CA), Italy
http://www.bioinformatica.crs4.it/
___
